For those looking into this article in the future - yes this is possible, but you must configure DrivePool to use the NtfsFilters rather than bypassing them and going straight to disk.
From article:
http://community.covecube.com/index.php?/topic/962-server-2012-r2-data-deduplication-w-drivepool/
However, you will need to make one change first to ensure that it works properly:
http://wiki.covecube.com/StableBit_DrivePool_2.x_Advanced_Settings
Set "CoveFs_BypassNtfsFilters" to "false", and reboot the system.
I am currently receiving up to 70% savings from deduplication, and have 3 drives in my pool.